Porous substrates may be used to facilitate the capture, stabilization, and storage of biological fluid samples. Pharmaceutical research involving blood testing, and forensic analysis of biological fluids collected using buccal swabs, are two examples in which substrates may be employed as a vehicle for the stabilization and storage of DNA. Such substrates may improve the long term stability of the DNA at room temperature and facilitate integration with an automated workflow. To process a sample deposited on a substrate, a portion of the substrate containing the sample is separated from the substrate (e.g., punched out). The punched out portion may be added to reagents and analyzed. It may be important to accurately locate the punch on the substrate (e.g., in case another punch needs to be taken from the same sample in the future). Moreover, the number of samples, such as DNA samples, that are being sent to forensic DNA data banking labs is increasing, and it would therefore be desirable to provide systems and methods to facilitate an automated processing of biological samples in an accurate and consistent manner.